CRR Metric for R2R
Maddee Rubenson (FlowWest)
2022-11-09
Run fallRunDSM model
s <- fall_run_model(mode = "seed")
sim <- fall_run_model(seeds = s, mode = "simulate")Adult Return Ratio
Definition: This value represents the proportion of natural spawners created by in river spawners from three years prior.
Calculation: Adult return to natural origin/spawning adult ratio (mean) is defined as: the number of natural origin adult returns in year X + 3 divided by the number of in-river spawners in year X.
\(natural origin adults _ (x+3) / in river spawners_x\)
Assumptions:
Adults return over the course of three years with 25% returning in year X + 2, 50% returning in year X + 3, and the final 25% returning in year X + 4. For example, in year 6 adults are returning from years 2 (25%), 3 (50%), and 4 (25%). This should be considered when exploring the adult return ratio because each year’s value is an aggregate of multiple years of return salmonids.
Values as
NAdo not have spawning
natural_spawners <- (sim$proportion_natural * sim$spawners) |>
as_tibble() |>
mutate(watershed = fallRunDSM::watershed_labels) |>
pivot_longer(names_to = "year", values_to = "natural_spawners", -watershed)
in_river_spawners <- sim$spawners |>
as_tibble() |>
mutate(watershed = fallRunDSM::watershed_labels) |>
pivot_longer(names_to = "year", values_to = "total_spawners", -watershed)
sim_spawners <- in_river_spawners |>
left_join(natural_spawners) |>
group_by(watershed) |>
mutate(
year = as.numeric(year),
lag_total = lag(total_spawners, 3),
origin_year = lag(year, 3),
metric = natural_spawners / lag_total)
adult_plot <- sim_spawners |>
ggplot(aes(origin_year, metric)) +
geom_line(aes(color = watershed)) +
scale_x_continuous(breaks = 1:20) +
theme_minimal() +
ylab('Adult Return Ratio')
ggplotly(adult_plot) # theme(legend.position = "top")
# 20 year average across all watersheds
# percents
sim_spawners |>
group_by(watershed) |>
summarise(
mean_adult_return_to_origin = mean(metric, na.rm = TRUE) * 100,
median_adult_return_to_origin = median(metric, na.rm = TRUE) * 100
) |> knitr::kable(digits = 1)| watershed | mean_adult_return_to_origin | median_adult_return_to_origin |
|---|---|---|
| American River | 16.6 | 15.2 |
| Antelope Creek | 133.1 | 63.7 |
| Battle Creek | 0.5 | 0.4 |
| Bear Creek | 142.3 | 82.6 |
| Bear River | 134.0 | 92.0 |
| Big Chico Creek | 140.3 | 69.6 |
| Butte Creek | 86.3 | 53.5 |
| Calaveras River | 129.9 | 73.4 |
| Clear Creek | 51.2 | 26.7 |
| Cosumnes River | 111.7 | 81.3 |
| Cottonwood Creek | 101.9 | 52.7 |
| Cow Creek | 58.8 | 25.2 |
| Deer Creek | 75.4 | 37.6 |
| Elder Creek | 218.4 | 119.5 |
| Feather River | 16.6 | 11.4 |
| Lower Sacramento River | NaN | NA |
| Lower-mid Sacramento River | NaN | NA |
| Merced River | 9.2 | 3.5 |
| Mill Creek | 64.7 | 29.3 |
| Mokelumne River | 2.8 | 1.2 |
| Paynes Creek | 136.7 | 74.5 |
| San Joaquin River | NaN | NA |
| Stanislaus River | 20.6 | 10.3 |
| Stony Creek | 163.8 | 98.2 |
| Sutter Bypass | NaN | NA |
| Thomes Creek | 158.9 | 72.3 |
| Tuolumne River | 14.8 | 10.9 |
| Upper Sacramento River | 55.3 | 26.6 |
| Upper-mid Sacramento River | NaN | NA |
| Yolo Bypass | NaN | NA |
| Yuba River | 36.7 | 28.6 |
Juveniles to Adult Ratio
Definition: This ratio represents the percent of returning natural origin adults that a cohort of juveniles produces.
Calculation: The average juvenile to adult return ration is defined as the number of juveniles produced in year X divided by the number of natural origin adult returns in year X + 3.
\(juveniles_x / natural origin adults_(x_+3)\)
Assumptions:
The number of juveniles produced is assumed to be the value prior to survival and migration factors applied. TODO: Do we want to capture total juveniles prior to or after survival metrics are applied?
Values as
NAdo not have spawning
juveniles <- sim$juveniles |>
as_tibble() |>
mutate(year = as.numeric(year)) |>
group_by(year, watershed) |>
summarise(total_juveniles = sum(juveniles)) |>
ungroup() |>
left_join(natural_spawners |>
mutate(year = as.numeric(year))) |>
arrange(watershed, year) |>
group_by(watershed) |>
mutate(natural_spawners_lag = lead(natural_spawners, 3),
metric = total_juveniles / natural_spawners_lag,
metric_rev = natural_spawners_lag / total_juveniles) |>
ungroup()
juveniles |>
group_by(watershed) |>
summarise(avg_juvenile_metric_perc = mean(metric_rev, na.rm = TRUE) * 100,
median_juvenile_metric_perc = median(metric_rev, na.rm = TRUE) * 100) |>
arrange(-avg_juvenile_metric_perc) |>
knitr::kable(digits = 1)| watershed | avg_juvenile_metric_perc | median_juvenile_metric_perc |
|---|---|---|
| Elder Creek | 0.5 | 0.3 |
| Stony Creek | 0.4 | 0.2 |
| Thomes Creek | 0.4 | 0.2 |
| Cottonwood Creek | 0.3 | 0.3 |
| Bear Creek | 0.3 | 0.2 |
| Big Chico Creek | 0.3 | 0.2 |
| Calaveras River | 0.3 | 0.2 |
| Paynes Creek | 0.3 | 0.2 |
| Bear River | 0.3 | 0.2 |
| Antelope Creek | 0.3 | 0.1 |
| Cosumnes River | 0.3 | 0.2 |
| Butte Creek | 0.2 | 0.1 |
| Deer Creek | 0.2 | 0.1 |
| Upper Sacramento River | 0.2 | 0.1 |
| Mill Creek | 0.2 | 0.1 |
| Cow Creek | 0.1 | 0.1 |
| Clear Creek | 0.1 | 0.1 |
| Feather River | 0.1 | 0.0 |
| Yuba River | 0.1 | 0.1 |
| Stanislaus River | 0.1 | 0.0 |
| American River | 0.0 | 0.0 |
| Tuolumne River | 0.0 | 0.0 |
| Merced River | 0.0 | 0.0 |
| Battle Creek | 0.0 | 0.0 |
| Mokelumne River | 0.0 | 0.0 |
| Lower Sacramento River | NaN | NA |
| Lower-mid Sacramento River | NaN | NA |
| San Joaquin River | NaN | NA |
| Sutter Bypass | NaN | NA |
| Upper-mid Sacramento River | NaN | NA |
| Yolo Bypass | NaN | NA |
juv_plot <- juveniles |>
ggplot(aes( year, metric_rev)) +
geom_line(aes(color = watershed)) +
scale_x_continuous(breaks = 1:20) +
ylab('Juvenile to Adult Ratio') +
theme_minimal()
ggplotly(juv_plot)